(...under (re)construction, paper commentaries are from the the old joint publications page ...)

Ashwin's new placement paper

Sungwooks 2D surface crystallization paper.

Cody and Ebbe's RNA origami science paper

Commentary with Ebbe.

Sturdier tubes with Deborah

Put very old grubbs paper at end.

Sungwook's PhD Thesis:
Beyond Watson and Crick: Programming the Self-Assembly and Reconfiguration of DNA Nanostructures Based on Stacking Interactions. *
144 pages. California Institute of Technology. Submitted May 2013. Sungwook Woo. Thesis advisor: Paul W.K. Rothemund.
Central to DNA nanotechnology is the Watson-Crick base pair. The
exquisite specificity, predictable strength, and combinatorial
diversity of hybridization reactions based on complementary DNA
sequences is what enables us to create sophisticated molecular
programs. But what other bases for complementary binding interactions
might there be? Might we be able to construct a new type of bonding
with the specificity and combinatorial diversity of DNA hybridization,
but which has new and different properties, perhaps allowing for
easier reconfiguration of self-assembled nanomachine parts? In his
PhD thesis, Sungwook starts from the simple observation that DNA
origami stick together at their edges via blunt-end stacking, and
constructs and studies a new system for combining origami based on
binary- and shape-coded stacking interactions. Sungwook applies
stacking interactions towards two different goals: the creation of
large two-dimensional origami crystals on surfaces, and the
origanization of expanding protein filaments to create large-scale
self-assembled geometries. Just as strand displacement enabled a whole
host of molecular programs which were unavailable to simple
equilibrium DNA hybridization, perhaps programmable stacking bonds will enable
a class of new molecular programs which undergo large scale
geometric rearrangement.
[ PhD thesis, 46 MB
(better @ 82 MB);
Caltech ETD.]

An Information-Bearing Seed for Nucleating Algorithmic Self-Assembly.* Robert D. Barish, Rebecca Schulman, Paul W. K. Rothemund, and Erik Winfree.
What is a seed? The tiny seed of a giant sequoia tree, sprouting
after the fire. The invisible seed of an idea, from which a thousand
possibilities grow. A crystal seed, determining the order of all that
grows from it. The seed of man and woman, carrying with it the future
of humanity. Clearly, it's important stuff. Why? The seed carries
the information, the creative part, the inspiration -- and what
follows is mere mechanism, the consequences, the algorithm. In this
work, we use DNA origami as a highly effective seed for growing DNA
tile crystals. Arbitrary information can be put on the seed; it
directs the growth of DNA crystals and determines their
morphology... much as a genome determines phenotype of an
organism... or even, as an idea creates the future.
[PNAS,
106: 6054-6059, 2009
(6 pages): .pdf, 1.7 MB,
supplementary information, 2.6 MB, and
appendix, 124 KB. ]
(Comments in the press:
Caltech Press Release,
New Scientist,
Foresight
)

An autonomous polymerization motor powered by DNA hybridization.* Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, Niles A. Pierce.
Can a DNA molecule walk? Can we design a molecular motor from scratch?
If so, how could it work? Consider macroscopic motors for a minute:
they come in all varieties, using all sorts of principles -- internal
combustion engines, steam engines, Wankel rotary engines, electric
motors, pneumatic motors, solenoids, rockets, jets... each best suited
to different tasks. The molecular world has similar diversity. In
biology, we see rotary motors like ATPase and the flagellar motor,
walking motors like kinesin, linear motors like RNA polymerase and the
ribosome, and waving motors like cilia. Not to mention muscle. Among
the most mind-bending are the polymerization motors of pathogenic
bacteria, such as Rickettsia and Listeria, that live inside eukaryotic
host cells. By displaying proteins that catalyze the polymerization
of the host cell's actin, these bacteria create a "comet tail" behind
them that pushes them forcefully through the cell and even into
neighboring cells. This was the motor principle targeted in our work,
which was lead by Niles' group. Perhaps most fascinating is that the DNA
polymers grow by insertion between the polymer tail and the DNA
catalyst strands anchored on the "surrogate bacterial cell". This
insertion takes place by a series of conformational rearrangements
without ever the two sides losing their strong attachment to each
other. Quite a dance!
[Nature Nanotechnology,
(vol. 2, pp. 490-494, 2007)
(5 pages): .pdf, 738 KB and
supplementary information, 581 KB.
]

Folding DNA to create nanoscale shapes and patterns.* Paul W. K. Rothemund
Paul sends a swarm of staple strands to tie viral DNA in knots...thereby self-assembling 100 x 100 nm objects
with roughly 6 nm resolution from the 7 kilobase single-stranded genomic DNA of M13mp18.
Rectangles. Squares. Triangles. Stars. Even a smiley-face. About 50 billion copies of each, in a typical reaction,
and with very high yields. It works like magic.
We did some calculations... Paul's smiley faces constitute the most concentrated happiness ever experienced on earth.
Each spot in such a structure contains a unique address and can be addressed as such by DNA hybridization, allowing
one to "write" on the DNA origami objects. Words. Pictures. Snowflakes. A map of North and South America.
We did some more calculations... Paul probably made more maps than have ever been produced in the history of mankind
-- we're definitely talking quantity over quality here. The applications of this technology are likely to be
less whimsical. For example, it can be used as a "nanobreadboard" for attaching almost arbitrary nanometer-scale components,
and there are few other ways to obtain such precise control over the arrangement of components at this scale.
You'll never look at M13 phage DNA the same way again...
[Nature440, 297-302 (16 March 2006).
article, .pdf, 575 KB. News and View, .pdf, 300 KB.
Supplementary material: .pdf, part 1, 6.3 MB; .pdf, part 2, 193 KB.
Caltech's Press Release.
]

Algorithmic Self-Assembly of DNA Sierpinski Triangles.* Paul W. K. Rothemund, Nick Papadakis, Erik Winfree.
Our first demonstration of algorithmic crystals, wherein
molecularly-encoded information directs the growth process to create a complex pattern.
The DNA crystals are, at the molecular level, a two-dimensional woven fabric of short DNA strands.
Both because this programmable growth could be considered a super-simplified toy model of
organismal development, and because DNA is the central information molecule in biology,
I like to call it "weaving the tapestry of life".
This is a substantial personal victory for me: I proposed that this
should be possible in 1995 as a graduate student -- nearly 10 years
later, Paul's efforts made it actually happen.
[PLoS Biology 2 (12) e424, 2004,
(13 pages): .pdf, 4.6 MB.]
See also our Extra Supplementary Materials page.
(PLoS Biology has a
synopsis
and a
primer by Chengde Mao for this paper.
Also it was highlighted
in Nature by Philip Ball.
And there's a
Caltech Press Release.
)

Design and Characterization of Programmable DNA Nanotubes.* Paul W. K. Rothemund, Axel Ekani-Nkodo, Nick Papadakis, Ashish Kumar,
Deborah Kuchnir Fygenson, Erik Winfree.
DNA tiles designed to make sheets sometimes roll up into tubes that are abstractly analogous to
protein microtubules that self-assemble from tubulin. Way cool! Fortuitously discovered during
Paul's work on the DNA Sierpinski triangles, DNA nanotubes have opened up a whole host of
interesting possibilities that we never dreamed of before...
[JACS 126(50):16344-16353, 2004,
(9 pages): article, 891 KB,
supp, 5.5 MB.]
See also our Extra Supplementary Materials page.

[Note added Feb. 2013: We presented a correct equation for the persistence length of a DNA tube but gave an incorrect derivation. Here is the erratum stating
changes to the paper and the correction to the supplementary information
which gives a valid proof. Remember kids, area moment of inertia is for bending,
mass moment of inertia is for spinning ice skaters!]

Self-Assembled Circuit Patterns.*Matthew Cook, Paul W. K. Rothemund, and Erik Winfree.
Can DNA self-assembly be used for patterning, as a scaffold for functional devices such as
molecular electronic circuits? We show that several circuit patterns, including demultiplexers,
random-access memory, and Hadamard matrix transforms, can be self-assembled (in principle) from
a small number of tile types.
[in DNA Computers 9,
LNCS volume 2943:91-107, 2004.
(17 pages, in color):
.pdf, 608 KB,
.ps, 3.2 MB]

Paul's PhD Thesis: Theory and Experiments in Algorithmic Self-Assembly.*
283 pages, in black and white. University of Southern California, December 2001. Paul W. K. Rothemund. Thesis advisor: Leonard Adleman.
This thesis describes theory on the uniqueness of self-assembled structures with an expanded account of material in the
paper "The Program-Size Complexity of Self-Assembled Squares" (see below),
experiments in algorithmic capillary force-based self-assembly as well as capillary
force-based assembly of Penrose tilings,
and DNA computation for breaking the Data Encryption Standard (DES).
It has appendices detailing the frequency of
certain tile configurations (vertex stars) in the Penrose tiling
and an initial experiment in making capillary force-based gears.
[pwkr_thesis_nov15.ps, 49.8 MB, or
pwkr_thesis_nov15.ps.gz, 8.8 MB, or
pwkr_thesis_nov15.pdf, 9.1 MB]

Using lateral capillary forces to compute by self-assembly. * Paul W. K. Rothemund.
Here Paul used macroscopic plastic tiles to test ideas about algorithmic self-assembly. The
plastic tiles self-assemble at the interface of oil and water, and hydrophilic and hydrophobic
patches on the edges of the tiles mediate the specific binding interactions between them. Tiles in this
paper encode binding interactions for creating Sierpinski triangles as well as Penrose tilings. Paul had mild
success creating unnucleated patterns with Sierpinski tiles and perhaps created the most complex
set of specific capillary bonds ever made.
[in Proceedings of the National Academy of Sciences, 97(3): 984-989, 2000, (6 pages):
Rothemund-PNAS-capillary.pdf, 911KB]

A DNA and restriction enzyme implementation of Turing Machines.* Paul W. K. Rothemund.
Here Paul gives a construction for simulating Minsky's 4 symbol, 7 state universal
Turing machine using DNA, the type IIS restriction enzyme Fok I, and ligase.
The encoding of machine state and current symbol used in this paper was later used
by Kobi Benenson of Udi Shapiro's group to create DNA finite state machines and hence
such machines have been called Rothemund-Shapiro machines.
[in DNA Based Computers, pgs 75-120, 1996, (29 pages below):
dimacs.ps, 578KB, or
dimacs.pdf, 330KB]